Hi,
Thank you for your quick answer!
I’ll look into that, but they share the same hosts-file and the
DHCP-server sets their hostname.
However I came across a setting in the slurm.conf-file ”Tmpfs” and
there were a note regarding it in the guide of mpi at the slurms
webpage. I implemented the proposed changes but still no luck.
Best regards,
Palle
------------------------------------------------------------------------
*From:* "slurm-users" <slurm-users-boun...@lists.schedmd.com>
*Sent:* 16 juli 2019 12:32
*To:* "Slurm User Community List" <slurm-users@lists.schedmd.com>
*Subject:* Re: [slurm-users] Running pyMPI on several nodes
srun: error: Application launch failed: Invalid node name specified
Hearns Law. All batch system problems are DNS problems.
Seriously though - check out your name resolution both on the head
node and the compute nodes.
On Tue, 16 Jul 2019 at 08:49, Pär Lundö < par.lu...@foi.se
<mailto:par.lu...@foi.se>> wrote:
Hi,
I have now had the time to look at some of your suggestions.
First I tried running "srun -N1 hostname" via a sbatch-script,
while having two nodes up and running.
"sinfo" yields that two nodes are up and idle prior to
submitting the sbatch-script.
After submitting the job, I receive an error stating that:
"srun: error: Task launch for 86.0 failed on node lxclient11:
Invalid node name specified.
srun: error: Application launch failed: Invalid node name specified
srun: Job step aborted: Waiting up to 32 seconds for job step
to finish.
srun: error: TImed out waiting for job step to complete"
From the log file at the client I get a more detailed error:
" Launching batch job 86 for UID 1000
[86.batch] error: Invalid host_index -1 for job 86
[86.batch] error: Host lxclient10 not in hostlist lxclient11
[86.batch] task_pre_launch: Using sched_affinity for tasks
rpc_launch_tasks: Invalid node list (lxclient10 not in lxclient11)"
My two nodes are called lxclient10 and lxclient11.
Why is my batch job launched with the UID 1000, shouldnt it be
launched via the slurm-user (which in my case has the UID 64030)?
What is meant by that the different nodes are not in the
nodeslist?
The two nodes and the server share the same setup of
IP-addresses in the "/etc/hosts"-file.
-> This was resolved due to that lxclient10 was noted as down.
Getting it back up, the submitting of the same sbatch-script,
resulted in no error.
However running it on two nodes I get an error
"srun: error: Job Step 88.0 aborted before step completely
launched.
srun: error: Job step aborted: Waiting up to 32 seconds for job
step to finish.
srun: error: task 1 launched failed: Unspecifed error
srun: error: lxclient10: task 0: Killed"
And in the slurmctld.log-file from the client I get an error
similiar to that prevously stated, that the pmix cannot bind
UNIX socket /var/spool/slurmd/stepd.slurm.pmix.88.0: Address
already in use (98)
I ran the lsof command, but I dont really know what I am
looking after, I can see if I grep with the different nodenames
that the two nodes have mounted the nfs-partition and that a
link is established.
"As an aside, you have checked that your username exists on
that compue server? getent passwd par
Also that your home directory is mounted - or something
substituting for your home directory?"
Yes, the user slurm exists on both nodes and have the same uid.
"Have you tried
srun -N# -n# mpirun python3 ....
Perhaps you have no MPI environment being setup for the
processes? There was no "--mpi" flag in your "srun" command
and we don't know if you have a default value for that or not.
"
In my slurm.conf-file I do specify that "MpiDefault=pmix" (And
it can be seen in the logfile that there is something wrong
with pmix, that the address already in use.)
One thing that struck my mind now is that I run these nodes as
a pair of diskless nodes, whom boots and mounts the same
filesystem which is supplied by a server. The run differen pids
for different processes which should not affect one another(?),
right?
Best regards,
Palle
On 2019-07-12 19:34, Pär Lundö wrote:
Hi,
Thank you so much for your quick responses!
It is much appreciated.
I dont have access to the cluster until next week, but I’ll
be sure to follow up on all of your suggestions and get
back you next week.
Have a nice weekend!
Best regards
Palle
------------------------------------------------------------------------
*From:* "slurm-users"
<slurm-users-boun...@lists.schedmd.com>
<mailto:slurm-users-boun...@lists.schedmd.com>
*Sent:* 12 juli 2019 17:37
*To:* "Slurm User Community List"
<slurm-users@lists.schedmd.com>
<mailto:slurm-users@lists.schedmd.com>
*Subject:* Re: [slurm-users] Running pyMPI on several nodes
Par, by 'poking around' Crhis means to use tools such as
netstat and lsof.
Also I would look as ps -eaf --forest to make sure there
are no 'orphaned' jusbs sitting on that compute node.
Having said that though, I have a dim memory of a classic
PBSPro error message which says something about a network
connection,
but really means that you cannot open a remote session on
that compute server.
As an aside, you have checked that your username exists on
that compue server? getent passwd par
Also that your home directory is mounted - or something
substituting for your home directory?
On Fri, 12 Jul 2019 at 15:55, Chris Samuel <
ch...@csamuel.org <mailto:ch...@csamuel.org>> wrote:
On 12/7/19 7:39 am, Pär Lundö wrote:
> Presumably, the first 8 tasks originates from the
first node (in this
> case the lxclient11), and the other node (lxclient10)
response as
> predicted.
That looks right, it seems the other node has two
processes fighting
over the same socket and that's breaking Slurm there.
> Is it neccessary to have passwordless ssh
communication alongside the
> munge authentication?
No, srun doesn't need (or use) that at all.
> In addition I checked the slurmctld-log from both the
server and client
> and found something (noted in bold):
This is from the slurmd log on the client from the look
of it.
> *[2019-07-12T14:57:53.771][83.0] task_p_pre_launch:
Using sched affinity
> for tasks lurm.pmix.83.0: Address already in use[98]*
> [2019-07-12T14:57:53.682][83.0] error: lxclient[0]
/pmix.server.c:386
> [pmix_stepd_init] mpi/pmix: ERROR:
pmixp_usock_create_srv
> [2019-07-12T14:57:53.683][83.0] error: (null) [0]
/mpi_pmix:156
> [p_mpi_hook_slurmstepd_prefork] mpi/pmix: ERROR:
pmixp_stepd_init() failed
That indicates that something else has grabbed the
socket it wants and
that's why the setup of the MPI ranks on the second
node fails.
You'll want to poke around there to see what's using it.
Best of luck!
Chris
--
Chris Samuel : http://www.csamuel.org/
<http://www.csamuel.org/> : Berkeley, CA, USA
